3 import jalview.jbgui.GAlignmentPanel;
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4 import jalview.schemes.*;
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5 import jalview.analysis.*;
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6 import jalview.datamodel.*;
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8 import java.awt.event.*;
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9 import java.awt.print.*;
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11 import com.sun.image.codec.jpeg.*;
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13 import java.awt.image.*;
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16 public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
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20 OverviewPanel overviewPanel;
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23 SecondaryStructurePanel ssPanel;
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24 public AlignFrame alignFrame;
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25 ScalePanel scalePanel;
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26 ScorePanel scorePanel;
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28 public AlignmentPanel(AlignFrame af, final AlignViewport av)
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32 seqPanel = new SeqPanel (av, this);
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33 idPanel = new IdPanel (av, this);
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34 scalePanel = new ScalePanel(av, this);
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35 scorePanel = new ScorePanel(av);
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36 ssPanel = new SecondaryStructurePanel(av);
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38 secondaryPanelHolder.add(ssPanel, BorderLayout.CENTER);
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39 idPanelHolder.add(idPanel, BorderLayout.CENTER);
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40 idPanel.addNotify();
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41 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
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42 scorePanelHolder.add(scorePanel, BorderLayout.CENTER);
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43 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
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44 setScrollValues(0,0);
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46 hscroll.addAdjustmentListener(this);
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47 vscroll.addAdjustmentListener(this);
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49 addComponentListener(new ComponentAdapter()
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51 public void componentResized(ComponentEvent evt)
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58 hscroll.setFocusable(false);
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59 vscroll.setFocusable(false);
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62 addKeyListener(new KeyAdapter()
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64 public void keyPressed(KeyEvent evt)
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66 switch(evt.getKeyCode())
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68 case 27: // escape key
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69 av.setRubberbandGroup(null);
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73 alignFrame.cut_actionPerformed(null);
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76 alignFrame.copy_actionPerformed(null);
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79 alignFrame.paste(true);
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82 alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
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84 case KeyEvent.VK_DOWN:
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85 alignFrame.moveSelectedSequences(false);
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87 case KeyEvent.VK_UP:
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88 alignFrame.moveSelectedSequences(true);
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91 alignFrame.findMenuItem_actionPerformed(null);
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99 public void highlightSearchResults(int [] results)
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101 seqPanel.seqCanvas.highlightSearchResults( results );
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103 // do we need to scroll the panel?
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104 if(results!=null && (av.getStartSeq()>results[0]
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105 || av.getEndSeq()<results[0]
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106 || av.getStartRes()>results[1]
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107 || av.getEndRes()<results[2]))
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108 setScrollValues(results[1], results[0]);
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114 public OverviewPanel getOverviewPanel()
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116 return overviewPanel;
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119 public void setOverviewPanel(OverviewPanel op)
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121 overviewPanel = op;
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125 public void setGraphPanelVisible(boolean b)
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127 idSpaceFillerPanel.setVisible(b);
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128 scorePanelHolder.setVisible(b);
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131 // bit annoying to call this twice, can you do better?
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135 public void setSecondaryStructureVisible(boolean b)
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137 secondaryPanelHolder.setVisible(b);
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141 public void setWrapAlignment(boolean wrap)
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143 scorePanelHolder.setVisible(!wrap);
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144 scalePanelHolder.setVisible(!wrap);
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145 secondaryPanelHolder.setVisible(!wrap);
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147 hscroll.setVisible(!wrap);
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149 idSpaceFillerPanel.setVisible(!wrap);
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150 idSpaceFillerPanel1.setVisible(!wrap);
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157 public void setColourScheme()
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159 ColourSchemeI cs = av.getGlobalColourScheme();
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161 if(av.getConservationSelected())
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164 Alignment al = (Alignment)av.getAlignment();
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165 Conservation c = new Conservation("All",
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166 ResidueProperties.propHash, 3, al.getSequences(), 0,
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170 c.verdict(false, 100);
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171 ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
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173 av.setGlobalColourScheme( ccs );
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180 public void RefreshPanels()
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184 idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );
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186 if(av.getWrapAlignment())
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188 int max = av.alignment.getWidth()/ (seqPanel.seqCanvas.getWidth()/av.charWidth)+1;
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190 int h = (av.alignment.getHeight() + 2)*av.charHeight;
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191 vextent = seqPanel.seqCanvas.getHeight()/h;
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192 vscroll.setValues(0,vextent,0,max);
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196 setScrollValues(av.getStartRes(), av.getStartSeq());
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197 av.getConsensus(true);
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198 if(overviewPanel!=null)
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199 overviewPanel.updateOverviewImage();
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209 public void setScrollValues(int x, int y)
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211 hextent = seqPanel.seqCanvas.getWidth()/av.getCharWidth();
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212 vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();
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214 if(hextent+x > av.getAlignment().getWidth())
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215 x = av.getAlignment().getWidth()- hextent;
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217 if(vextent+y > av.getAlignment().getHeight())
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218 y = av.getAlignment().getHeight() - vextent;
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226 hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
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227 vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
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235 public void adjustmentValueChanged(AdjustmentEvent evt)
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238 if (evt.getSource() == hscroll)
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240 int x = hscroll.getValue();
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242 av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
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245 if (evt.getSource() == vscroll)
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247 int offy = vscroll.getValue();
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248 if (av.getWrapAlignment())
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250 av.setStartRes( vscroll.getValue() * av.getChunkWidth());
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254 av.setStartSeq(offy);
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255 av.setEndSeq(offy + seqPanel.seqCanvas.getHeight() / av.getCharHeight());
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260 if(overviewPanel!=null)
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261 overviewPanel.setBoxPosition();
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266 public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
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268 pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
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270 int pwidth = (int) pf.getImageableWidth();
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271 int pheight = (int) pf.getImageableHeight();
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273 if (av.getWrapAlignment())
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274 return printWrappedAlignment(pg, pwidth,pheight, pi);
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276 return printUnwrapped(pg,pwidth, pheight,pi);
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279 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
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282 int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();
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285 pg.setColor(Color.white);
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286 pg.fillRect(0,0,pwidth, pheight);
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287 pg.setFont( av.getFont() );
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289 ////////////////////////////////////
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290 /// How many sequences and residues can we fit on a printable page?
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291 int totalRes = (pwidth - idWidth)/av.getCharWidth();
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292 int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;
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293 int pagesWide = av.getAlignment().getWidth() / totalRes +1;
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294 int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;
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296 if (pi >= pagesWide*pagesHigh)
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297 return Printable.NO_SUCH_PAGE;
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299 /////////////////////////////
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300 /// Only print these sequences and residues on this page
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301 int startRes, endRes, startSeq, endSeq;
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302 startRes = (pi % pagesWide) * totalRes;
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303 endRes = startRes + totalRes-1;
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304 if(endRes>av.getAlignment().getWidth())
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305 endRes = av.getAlignment().getWidth();
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307 startSeq = (pi / pagesWide) * totalSeq;
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308 endSeq = startSeq + totalSeq;
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309 if(endSeq > av.getAlignment().getHeight())
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310 endSeq = av.getAlignment().getHeight();
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315 pg.translate(idWidth,0);
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316 scalePanel.scaleCanvas.drawScale(pg, startRes, endRes, pwidth-idWidth);
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318 pg.translate(-idWidth, 30);
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321 Color currentColor=null;
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322 Color currentTextColor=null;
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323 for(int i=startSeq; i<endSeq; i++)
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325 if (av.getSelection().contains(av.getAlignment().getSequenceAt(i)))
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327 currentColor = Color.gray;
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328 currentTextColor = Color.black;
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332 currentColor = av.getAlignment().getSequenceAt(i).getColor();
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333 currentTextColor = Color.black;
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336 pg.setColor(currentColor);
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337 pg.fillRect(0, jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),
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339 av.getCharHeight());
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341 pg.setColor(currentTextColor);
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343 String string = av.getAlignment().getSequenceAt(i).getDisplayId();
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344 pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight
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345 (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));
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348 // draw main sequence panel
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349 pg.translate(idWidth,0);
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350 pg.setClip(0,0,pwidth-idWidth, pheight);
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351 seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);
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353 return Printable.PAGE_EXISTS;
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357 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
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360 int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();
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362 if( seqPanel.seqCanvas.getWidth() < pwidth-idWidth)
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363 pwidth = seqPanel.seqCanvas.getWidth() + idWidth;
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366 pg.setColor(Color.white);
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367 pg.fillRect(0,0,pwidth, pheight);
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368 pg.setFont( av.getFont() );
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370 ////////////////////////////////////
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371 /// How many sequences and residues can we fit on a printable page?
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372 AlignmentI da = av.alignment;
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373 int endy = da.getHeight();
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374 int chunkHeight = (da.getHeight() + 2)*av.charHeight;
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375 int chunkWidth = (pwidth-idWidth)/av.charWidth;
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377 int noChunksOnPage = pheight / chunkHeight;
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378 int totalChunks = da.getWidth() / chunkWidth;
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380 if ( pi*noChunksOnPage > totalChunks )
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381 return Printable.NO_SUCH_PAGE;
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385 pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight);
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387 int row = pi*noChunksOnPage;
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388 pg.setColor(Color.black);
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389 for(int ypos=2*av.charHeight;
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390 ypos <= pheight && row*chunkWidth<da.getWidth();
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391 ypos += chunkHeight, row++ )
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393 for (int i = 0; i < endy; i++)
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395 SequenceI s = da.getSequenceAt(i);
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396 pg.drawString(s.getDisplayId(), 0,
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397 AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
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398 av.charHeight - (av.charHeight / 5));
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402 // draw main sequence panel
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403 pg.translate(idWidth,0);
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404 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth-idWidth, pheight, pi*noChunksOnPage*chunkWidth);
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407 return Printable.PAGE_EXISTS;
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411 public void makeJPG(int width, int height)
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416 BufferedImage bi = new BufferedImage(width, height,
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417 BufferedImage.TYPE_INT_RGB);
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418 Graphics pg = bi.getGraphics();
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422 if (av.getWrapAlignment())
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423 printWrappedAlignment(pg, width, height, 0);
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425 printUnwrapped(pg, width, height, 0);
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427 catch (Exception ex)
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430 javax.swing.JFileChooser chooser = new javax.swing.JFileChooser(jalview.bin.Cache.getProperty(
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431 "LAST_DIRECTORY"));
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432 chooser.setDialogTitle("Create JPG image from alignment");
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433 chooser.setToolTipText("Save");
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435 int value = chooser.showSaveDialog(this);
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436 if (value == javax.swing.JFileChooser.APPROVE_OPTION)
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439 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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440 JPEGImageEncoder jie = JPEGCodec.createJPEGEncoder(out);
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441 JPEGEncodeParam param = JPEGCodec.getDefaultJPEGEncodeParam(bi);
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442 param.setQuality(1.0f, true);
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444 jie.encode(bi, param);
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449 catch (IOException ex)
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451 System.out.println("ex Writing image ");
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